生物数据分析

通用的软件

perl,R, biopython, bioperl, bioconductor

序列比对

bowtie, bowtie2, bwa, blast, SOAPaligner,MUMmer, muscle, clustalw, blat, mega

过滤和质控

FastQC, fastx-toolkit, NGS-QC-Toolkits, perlinhouse

转录组分析

Trinity, Oases, tophat, cufflinks, RSEM, eXpress, cumRound, DEseq, edgeR, misa, primer3_core, cd-hit

基因组组装

ALLPATH-LG, SOAPdenovo, SOAPdenovo2,newbler,SSPACEs, velvet, ABySS, gapfiller, edena,

简化基因组

velvet, Rainbow

宏基因组16s

mothur, qiime, metasee, pandaseq, flash

基因芯片

TM4, J-Express、Scanalyze、KNNImpute

蛋白组分析

ReAdW, TPP, GPM

microRNA分析

targetscan, pstarget, miRanda,mfold,randfold, RNAhybrid,RNA22,miRNAkey, mirdeep2,RNAstructure

Chip-seq分析

cisgenome, macs

全基因组甲基化

PeakSeq, FindPeaks, BSMAP, BSSeeker

重测序分析

Bwa, SOAP, bowtie(bowtie2), Samtools, GATK, bedtools

基因组注释

genescan, genemark, glimmers, AUGUSTUS

功能注释

Blast2GO, Interproscan, PfamScan, HMMMER

重复序列注释

RepeatMasker, RepeatModeler, RECON, RepeatScout,TRF

比较基因组学

CONTIGuator, Act, Mauve

群体遗传学

HaploView,plink,gplink,tassel

其他

Circos, IGV, Tablet, Weblogo, Cytoscape, psRobot, promoter